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Background   Anaplasma phagocytophilum  is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As  A. phagocytophilum  is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain.  Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with  A. phagocytophilum  isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains.    Results  DNA was extracted from a bovine blood sample infected by  A. phagocytophilum . Following a whole genome capture approach,  A. phagocytophilum  DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the  A. phagocytophilum  genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced  A. phagocytophilum  genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the  A. phagocytophilum  bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function” and require further analysis. We also identified nine proteins common to both European domestic ruminants tested.    Conclusion  Using a whole genome capture approach, we have sequenced the first  A. phagocytophilum  genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the  A. phagocytophilum  bovine genome could be involved in host tropism, therefore their functions need to be explored.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-973) contains supplementary material, which is available to authorized users.

Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture